############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:openCyto.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings openCyto_2.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/openCyto.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘openCyto/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘openCyto’ version ‘2.6.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘openCyto’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.8Mb sub-directories of 1Mb or more: libs 4.5Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘flowViz’ All declared Imports should be used. Unexported objects imported by ':::' calls: ‘flowClust:::.ellipsePoints’ ‘flowStats:::drvkde’ ‘flowWorkspace:::.addGate’ ‘flowWorkspace:::.cpp_addGate’ ‘flowWorkspace:::.cpp_boolGating’ ‘flowWorkspace:::.cpp_setIndices’ ‘flowWorkspace:::.getAllDescendants’ ‘flowWorkspace:::filter_to_list.booleanFilter’ ‘flowWorkspace:::filter_to_list.rectangleGate’ ‘lattice:::updateList’ ‘ncdfFlow:::toBitVec’ ‘ncdfFlow:::toLogical’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘groupBy’ ‘isCollapse’ ‘ppMethod’ ‘unlockNamespace’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Found the following possibly unsafe calls: File ‘openCyto/R/pluginFramework.R’: unlockBinding(methodName, ENV) unlockBinding(methodName, ENV) .boundary: no visible global function definition for ‘rectangleGate’ .center_mode: no visible global function definition for ‘density’ .find_peaks: no visible global function definition for ‘density’ .find_peaks: no visible global function definition for ‘points’ .find_valleys: no visible global function definition for ‘density’ .gateToFilterResult: no visible global function definition for ‘exprs’ .gateToFilterResult: no visible global function definition for ‘as’ .gate_tail: no visible global function definition for ‘exprs’ .gate_tail: no visible global function definition for ‘exprs<-’ .gate_tail: no visible global function definition for ‘rectangleGate’ .gatingTemplate: no visible global function definition for ‘as’ .gatingTemplate: no visible global function definition for ‘new’ .gatingTemplate: no visible binding for global variable ‘pop’ .gatingTemplate: no visible binding for global variable ‘gating_method’ .gatingTemplate: no visible binding for global variable ‘gating_args’ .gatingTemplate: no visible binding for global variable ‘collapseDataForGating’ .gatingTemplate: no visible binding for global variable ‘preprocessing_method’ .gatingTemplate: no visible binding for global variable ‘preprocessing_args’ .gatingTemplate: no visible global function definition for ‘extends’ .gating_adaptor: no visible global function definition for ‘as’ .gating_adaptor: no visible global function definition for ‘na.omit’ .gating_adaptor: no visible global function definition for ‘rectangleGate’ .gating_adaptor: no visible global function definition for ‘filters’ .gating_adaptor: no visible global function definition for ‘extends’ .gating_gtMethod: no visible global function definition for ‘na.omit’ .gating_gtMethod : : no visible global function definition for ‘extends’ .gating_gtMethod: no visible global function definition for ‘extends’ .gating_gtMethod: no visible global function definition for ‘is’ .gating_gtMethod : : no visible global function definition for ‘filters’ .gating_refGate : : no visible global function definition for ‘rectangleGate’ .gating_refGate: no visible global function definition for ‘filterList’ .gating_refGate: no visible global function definition for ‘is’ .gen_1dgate : : no visible binding for global variable ‘parent’ .gen_1dgate : : no visible binding for global variable ‘gating_method’ .gen_1dgate : : no visible binding for global variable ‘gating_args’ .gen_1dgate : : no visible binding for global variable ‘collapseDataForGating’ .gen_1dgate : : no visible binding for global variable ‘preprocessing_method’ .gen_1dgate : : no visible binding for global variable ‘preprocessing_args’ .gen_dummy_ref_gate: no visible binding for global variable ‘parent’ .gen_dummy_ref_gate : : no visible binding for global variable ‘pop’ .gen_dummy_ref_gate : : no visible binding for global variable ‘gating_method’ .gen_dummy_ref_gate : : no visible binding for global variable ‘gating_args’ .gen_dummy_ref_gate : : no visible binding for global variable ‘collapseDataForGating’ .gen_dummy_ref_gate : : no visible binding for global variable ‘preprocessing_method’ .gen_dummy_ref_gate : : no visible binding for global variable ‘preprocessing_args’ .gen_refGate: no visible binding for global variable ‘parent’ .gen_refGate: no visible binding for global variable ‘gating_args’ .getEllipse: no visible global function definition for ‘qf’ .getEllipse: no visible global function definition for ‘qchisq’ .getEllipseGate: no visible global function definition for ‘qf’ .getEllipseGate: no visible global function definition for ‘qchisq’ .getEllipseGate: no visible global function definition for ‘polygonGate’ .getEllipseGate: no visible global function definition for ‘ellipsoidGate’ .getFullPath: no visible binding for global variable ‘parent’ .improvedMindensity: no visible global function definition for ‘density’ .improvedMindensity: no visible global function definition for ‘smooth.spline’ .improvedMindensity: no visible global function definition for ‘predict’ .improvedMindensity: no visible global function definition for ‘median’ .improvedMindensity : .plots: no visible global function definition for ‘abline’ .improvedMindensity: no visible global function definition for ‘par’ .improvedMindensity: no visible global function definition for ‘abline’ .plotTree: no visible global function definition for ‘as’ .plotTree: no visible global function definition for ‘par’ .plotTree: no visible global function definition for ‘legend’ .preprocess_csv: no visible binding for global variable ‘pop’ .preprocess_csv: no visible binding for global variable ‘parent’ .preprocess_csv: no visible binding for global variable ‘gating_method’ .preprocess_csv: no visible binding for global variable ‘gating_args’ .preprocess_csv: no visible binding for global variable ‘collapseDataForGating’ .preprocess_csv: no visible binding for global variable ‘preprocessing_method’ .preprocess_csv: no visible binding for global variable ‘preprocessing_args’ .preprocess_row: no visible binding for global variable ‘pop’ .preprocess_row: no visible binding for global variable ‘gating_method’ .preprocess_row: no visible binding for global variable ‘parent’ .preprocess_row: no visible binding for global variable ‘gating_args’ .preprocess_row: no visible binding for global variable ‘preprocessing_method’ .preprocess_row: no visible binding for global variable ‘preprocessing_args’ .prior_flowClust1d: no visible global function definition for ‘fsApply’ .prior_flowClust1d : : no visible global function definition for ‘exprs’ .prior_flowClust1d: no visible global function definition for ‘hclust’ .prior_flowClust1d: no visible global function definition for ‘dist’ .prior_flowClust1d: no visible global function definition for ‘median’ .prior_flowClust1d: no visible global function definition for ‘cutree’ .prior_flowClust1d: no visible global function definition for ‘kmeans’ .prior_flowClust1d : : no visible global function definition for ‘sd’ .prior_flowClust1d: no visible binding for global variable ‘var’ .prior_flowClust1d : : no visible global function definition for ‘embed’ .prior_flowClust1d : : no visible binding for global variable ‘var’ .prior_kmeans : : no visible global function definition for ‘exprs’ .prior_kmeans : : no visible global function definition for ‘kmeans’ .prior_kmeans : : : no visible global function definition for ‘cov’ .prior_kmeans : : no visible global function definition for ‘dist’ .prior_kmeans: no visible binding for global variable ‘cov.wt’ .quadGate2rectangleGates: no visible global function definition for ‘rectangleGate’ .quadGate2rectangleGates: no visible global function definition for ‘filters’ .quantile_flowClust : cdf_target : : no visible global function definition for ‘pt’ .quantile_flowClust : cdf_target: no visible global function definition for ‘weighted.mean’ .quantile_flowClust: no visible global function definition for ‘uniroot’ .read.FCS.csv: no visible global function definition for ‘new’ .read.flowSet.csv: no visible global function definition for ‘flowSet’ .standardize_flowFrame: no visible global function definition for ‘exprs’ .standardize_flowFrame: no visible global function definition for ‘exprs<-’ .standardize_flowset: no visible global function definition for ‘fsApply’ .standardize_flowset: no visible global function definition for ‘flowSet’ .standardize_flowset: no visible global function definition for ‘as’ .tailgate: no visible global function definition for ‘exprs’ .tailgate: no visible global function definition for ‘exprs<-’ .tailgate: no visible global function definition for ‘rectangleGate’ .truncate_flowframe: no visible global function definition for ‘rectangleGate’ .truncate_flowframe: no visible global function definition for ‘Subset’ .truncate_flowset: no visible global function definition for ‘rectangleGate’ .truncate_flowset: no visible global function definition for ‘Subset’ .unique_check_alias: no visible binding for global variable ‘parent’ as.data.table.gatingTemplate : : no visible global function definition for ‘extends’ fast_coerce: no visible global function definition for ‘fsApply’ fast_coerce : : no visible global function definition for ‘exprs’ fast_coerce: no visible global function definition for ‘new’ fcEllipsoidGate: no visible global function definition for ‘as’ fcFilterList : : no visible global function definition for ‘extends’ fcFilterList: no visible global function definition for ‘filterList’ fcFilterList: no visible global function definition for ‘as’ fcPolygonGate: no visible global function definition for ‘as’ fcRectangleGate: no visible global function definition for ‘as’ fcTree: no visible global function definition for ‘as’ fcTree: no visible global function definition for ‘new’ gate_flowclust_1d: no visible global function definition for ‘exprs’ gate_flowclust_1d: no visible global function definition for ‘rectangleGate’ gate_flowclust_1d: no visible global function definition for ‘abline’ gate_flowclust_1d: no visible global function definition for ‘rainbow’ gate_flowclust_1d: no visible global function definition for ‘lines’ gate_flowclust_2d: no visible global function definition for ‘new’ gate_flowclust_2d: no visible global function definition for ‘dist’ gate_flowclust_2d: no visible global function definition for ‘qchisq’ gate_flowclust_2d: no visible global function definition for ‘exprs’ gate_flowclust_2d: no visible global function definition for ‘sd’ gate_flowclust_2d: no visible global function definition for ‘polygonGate’ gate_flowclust_2d: no visible global function definition for ‘lines’ gate_flowclust_2d: no visible global function definition for ‘points’ gate_mindensity: no visible global function definition for ‘exprs’ gate_mindensity: no visible global function definition for ‘rectangleGate’ gate_mindensity2: no visible global function definition for ‘exprs’ gate_mindensity2: no visible global function definition for ‘rectangleGate’ gate_quad_sequential : : no visible global function definition for ‘exprs’ gate_quad_sequential: no visible global function definition for ‘filter’ gate_quad_sequential: no visible global function definition for ‘as’ gate_quad_sequential : : no visible global function definition for ‘rectangleGate’ gate_quad_sequential: no visible global function definition for ‘filters’ gate_quad_tmix: no visible global function definition for ‘filter’ gate_quad_tmix: no visible global function definition for ‘as’ gate_quad_tmix: no visible global function definition for ‘polygonGate’ gate_quad_tmix: no visible global function definition for ‘filters’ gate_quantile: no visible global function definition for ‘exprs’ gate_quantile: no visible global function definition for ‘quantile’ gate_quantile: no visible global function definition for ‘hist’ gate_quantile: no visible global function definition for ‘density’ gate_quantile: no visible global function definition for ‘abline’ gate_quantile: no visible global function definition for ‘text’ gate_quantile: no visible global function definition for ‘rectangleGate’ gate_tail: no visible global function definition for ‘exprs’ gate_tail: no visible global function definition for ‘rectangleGate’ gate_tautstring: no visible global function definition for ‘exprs’ gate_tautstring: no visible global function definition for ‘rectangleGate’ gs_add_gating_method: no visible global function definition for ‘is’ gs_add_gating_method_init: no visible global function definition for ‘is’ gs_remove_gating_method: no visible global function definition for ‘is’ mindensity: no visible global function definition for ‘exprs’ mindensity: no visible global function definition for ‘rectangleGate’ ocRectRefGate: no visible global function definition for ‘as’ prior_flowclust : : no visible global function definition for ‘is’ quadGate.tmix: no visible global function definition for ‘quad_gate_tmix’ tailgate: no visible global function definition for ‘exprs’ tailgate: no visible global function definition for ‘rectangleGate’ coerce,ncdfFlowList-flowFrame: no visible global function definition for ‘selectMethod’ gatingTemplate,character: no visible binding for global variable ‘isMultiPops’ gatingTemplate,character: no visible binding for global variable ‘pop’ gatingTemplate,character: no visible binding for global variable ‘gating_args’ plot,fcFilterList-ANY : : no visible global function definition for ‘dnorm’ plot,fcFilterList-ANY: no visible global function definition for ‘hist’ plot,fcFilterList-ANY: no visible global function definition for ‘exprs’ plot,fcFilterList-ANY: no visible global function definition for ‘lines’ plot,fcFilterList-ANY: no visible global function definition for ‘rainbow’ plot,fcFilterList-ANY: no visible global function definition for ‘abline’ show,fcFilter: no visible global function definition for ‘callNextMethod’ Undefined global functions or variables: Subset abline as callNextMethod collapseDataForGating cov cov.wt cutree density dist dnorm ellipsoidGate embed exprs exprs<- extends filter filterList filters flowSet fsApply gating_args gating_method hclust hist is isMultiPops kmeans legend lines median na.omit new par parent points polygonGate pop predict preprocessing_args preprocessing_method pt qchisq qf quad_gate_tmix quantile rainbow rectangleGate sd selectMethod smooth.spline text uniroot var weighted.mean Consider adding importFrom("grDevices", "rainbow") importFrom("graphics", "abline", "hist", "legend", "lines", "par", "points", "text") importFrom("methods", "as", "callNextMethod", "extends", "is", "new", "selectMethod") importFrom("stats", "cov", "cov.wt", "cutree", "density", "dist", "dnorm", "embed", "filter", "hclust", "kmeans", "median", "na.omit", "predict", "pt", "qchisq", "qf", "quantile", "sd", "smooth.spline", "uniroot", "var", "weighted.mean") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.14-bioc/meat/openCyto.Rcheck/00check.log’ for details.